Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 85L7Y

Calculation Name: 4ONS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ONS

Chain ID: A

ChEMBL ID:

UniProt ID: Q61301

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2368767.128355
FMO2-HF: Nuclear repulsion 2278411.069657
FMO2-HF: Total energy -90356.058698
FMO2-MP2: Total energy -90617.418272


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:18:GLU)


Summations of interaction energy for fragment #1(A:18:GLU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-132.019-138.27329.487-12.608-10.6250.133
Interaction energy analysis for fragmet #1(A:18:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.845 / q_NPA : -0.910
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A20ARG10.8200.8641.814-138.882-145.23429.488-12.600-10.5370.133
4A21THR00.0370.0025.305-3.096-2.998-0.001-0.008-0.0880.000
5A22LEU00.0120.0198.526-2.699-2.6990.0000.0000.0000.000
6A23THR0-0.044-0.0289.928-3.235-3.2350.0000.0000.0000.000
7A24VAL00.0660.02511.194-1.757-1.7570.0000.0000.0000.000
8A25GLU-1-0.750-0.85511.11522.72222.7220.0000.0000.0000.000
9A26ARG10.9180.95313.811-23.120-23.1200.0000.0000.0000.000
10A27LEU0-0.022-0.00615.256-1.141-1.1410.0000.0000.0000.000
11A28LEU00.0070.01017.220-0.963-0.9630.0000.0000.0000.000
12A29GLU-1-0.860-0.89218.72512.89212.8920.0000.0000.0000.000
13A30PRO00.0400.02020.448-0.802-0.8020.0000.0000.0000.000
14A31LEU00.0080.00822.797-0.701-0.7010.0000.0000.0000.000
15A32VAL00.0110.01521.089-0.658-0.6580.0000.0000.0000.000
16A33THR0-0.001-0.03424.221-0.745-0.7450.0000.0000.0000.000
17A34GLN0-0.043-0.01026.103-0.268-0.2680.0000.0000.0000.000
18A35VAL0-0.033-0.01726.952-0.472-0.4720.0000.0000.0000.000
19A36THR0-0.024-0.01227.124-0.280-0.2800.0000.0000.0000.000
20A37THR0-0.017-0.01029.796-0.086-0.0860.0000.0000.0000.000
21A38LEU0-0.066-0.03232.165-0.175-0.1750.0000.0000.0000.000
22A39VAL0-0.0050.00735.454-0.297-0.2970.0000.0000.0000.000
23A52GLY00.0520.02648.402-0.062-0.0620.0000.0000.0000.000
24A53ARG10.8430.90943.461-6.858-6.8580.0000.0000.0000.000
25A54SER0-0.0080.01244.744-0.153-0.1530.0000.0000.0000.000
26A55LYS10.9970.97744.846-5.882-5.8820.0000.0000.0000.000
27A56LYS10.9720.97645.046-6.294-6.2940.0000.0000.0000.000
28A57ALA00.0340.03441.2280.1200.1200.0000.0000.0000.000
29A58HIS00.011-0.00540.3490.2420.2420.0000.0000.0000.000
30A59VAL0-0.0070.00540.4550.1260.1260.0000.0000.0000.000
31A60LEU0-0.0110.01038.3160.1310.1310.0000.0000.0000.000
32A61ALA00.0420.01736.1290.2290.2290.0000.0000.0000.000
33A62ALA0-0.001-0.00235.6180.2150.2150.0000.0000.0000.000
34A63SER0-0.034-0.02836.4330.0810.0810.0000.0000.0000.000
35A64VAL0-0.0040.00130.9770.1880.1880.0000.0000.0000.000
36A65GLU-1-0.800-0.87131.5229.7879.7870.0000.0000.0000.000
37A66GLN0-0.010-0.00131.8780.3370.3370.0000.0000.0000.000
38A67ALA00.0350.01630.9330.1660.1660.0000.0000.0000.000
39A68THR0-0.025-0.02226.6470.4500.4500.0000.0000.0000.000
40A69GLN0-0.024-0.02727.4910.5250.5250.0000.0000.0000.000
41A70ASN0-0.044-0.03528.8110.0720.0720.0000.0000.0000.000
42A71PHE00.0010.00320.9680.1800.1800.0000.0000.0000.000
43A72LEU00.0070.00223.2090.4360.4360.0000.0000.0000.000
44A73GLU-1-0.872-0.91324.55610.09010.0900.0000.0000.0000.000
45A74LYS10.8300.89825.134-10.118-10.1180.0000.0000.0000.000
46A75GLY00.0360.02721.0710.4080.4080.0000.0000.0000.000
47A76GLU-1-0.835-0.91220.62712.26512.2650.0000.0000.0000.000
48A77GLN0-0.080-0.03822.200-0.043-0.0430.0000.0000.0000.000
49A78ILE00.0280.01018.4430.1220.1220.0000.0000.0000.000
50A79ALA00.0170.01517.5850.5030.5030.0000.0000.0000.000
51A80LYS10.8220.90818.214-10.733-10.7330.0000.0000.0000.000
52A81GLU-1-0.821-0.90820.89311.40511.4050.0000.0000.0000.000
53A82SER0-0.0050.01015.051-0.149-0.1490.0000.0000.0000.000
54A83GLN00.0130.00816.696-0.508-0.5080.0000.0000.0000.000
55A84ASP-1-0.868-0.92211.88719.83619.8360.0000.0000.0000.000
56A85LEU00.012-0.0097.456-0.498-0.4980.0000.0000.0000.000
57A86LYS10.8050.89211.019-15.435-15.4350.0000.0000.0000.000
58A87GLU-1-0.909-0.94711.26918.98618.9860.0000.0000.0000.000
59A88GLU-1-0.795-0.8938.68525.39025.3900.0000.0000.0000.000
60A89LEU0-0.020-0.00711.189-0.776-0.7760.0000.0000.0000.000
61A90VAL00.0140.00114.326-0.892-0.8920.0000.0000.0000.000
62A91ALA0-0.011-0.00112.934-0.795-0.7950.0000.0000.0000.000
63A92ALA00.0070.00113.649-0.623-0.6230.0000.0000.0000.000
64A93VAL0-0.016-0.01015.416-0.790-0.7900.0000.0000.0000.000
65A94GLU-1-0.798-0.89518.23911.97011.9700.0000.0000.0000.000
66A95ASP-1-0.895-0.93416.69115.09915.0990.0000.0000.0000.000
67A96VAL00.000-0.00118.753-0.749-0.7490.0000.0000.0000.000
68A97ARG10.8090.88521.115-12.324-12.3240.0000.0000.0000.000
69A98LYS10.8600.92620.032-13.892-13.8920.0000.0000.0000.000
70A99GLN0-0.030-0.02219.820-1.003-1.0030.0000.0000.0000.000
71A100GLY00.0210.01223.814-0.453-0.4530.0000.0000.0000.000
72A101GLU-1-0.820-0.87326.5939.2879.2870.0000.0000.0000.000
73A102THR0-0.041-0.02625.791-0.450-0.4500.0000.0000.0000.000
74A103MET0-0.0280.00127.885-0.353-0.3530.0000.0000.0000.000
75A104ARG10.7750.86029.546-9.633-9.6330.0000.0000.0000.000
76A105ILE0-0.004-0.00330.746-0.367-0.3670.0000.0000.0000.000
77A106ALA00.0140.00531.756-0.292-0.2920.0000.0000.0000.000
78A107SER0-0.021-0.04332.912-0.253-0.2530.0000.0000.0000.000
79A108SER0-0.026-0.01035.332-0.283-0.2830.0000.0000.0000.000
80A109GLU-1-0.858-0.92536.5997.5527.5520.0000.0000.0000.000
81A110PHE0-0.034-0.01737.106-0.229-0.2290.0000.0000.0000.000
82A111ALA0-0.015-0.01738.956-0.199-0.1990.0000.0000.0000.000
83A112ASP-1-0.785-0.90141.2366.9036.9030.0000.0000.0000.000
84A113ASP-1-0.825-0.88142.6676.9896.9890.0000.0000.0000.000
85A114PRO00.0080.01741.8720.0570.0570.0000.0000.0000.000
86A115CYS0-0.032-0.02442.7860.0150.0150.0000.0000.0000.000
87A116SER0-0.003-0.01741.6210.0860.0860.0000.0000.0000.000
88A117SER00.031-0.00539.7460.1560.1560.0000.0000.0000.000
89A118VAL00.0310.02036.7870.2320.2320.0000.0000.0000.000
90A119LYS10.8680.94235.894-7.161-7.1610.0000.0000.0000.000
91A120ARG10.8760.94935.551-7.507-7.5070.0000.0000.0000.000
92A121GLY00.0260.00633.8120.2150.2150.0000.0000.0000.000
93A122THR0-0.039-0.03631.3670.4130.4130.0000.0000.0000.000
94A123MET00.0150.01930.6820.2490.2490.0000.0000.0000.000
95A124VAL0-0.006-0.00130.2820.2600.2600.0000.0000.0000.000
96A125ARG10.9100.95227.593-9.579-9.5790.0000.0000.0000.000
97A126ALA00.0350.02726.1720.4560.4560.0000.0000.0000.000
98A127ALA00.0300.00726.0500.3530.3530.0000.0000.0000.000
99A128ARG10.8310.91023.873-10.970-10.9700.0000.0000.0000.000
100A129ALA00.0230.02621.8940.6050.6050.0000.0000.0000.000
101A130LEU00.0260.00821.2950.6330.6330.0000.0000.0000.000
102A131LEU00.020-0.00222.0920.3960.3960.0000.0000.0000.000
103A132SER0-0.033-0.01218.5110.5420.5420.0000.0000.0000.000
104A133ALA00.0380.02617.4770.8990.8990.0000.0000.0000.000
105A134VAL0-0.039-0.02017.8090.5690.5690.0000.0000.0000.000
106A135THR0-0.030-0.02916.9730.2600.2600.0000.0000.0000.000
107A136ARG10.8070.8828.599-24.430-24.4300.0000.0000.0000.000
108A137LEU00.0130.00313.9591.0091.0090.0000.0000.0000.000
109A138LEU0-0.019-0.00915.6910.2080.2080.0000.0000.0000.000
110A139ILE0-0.021-0.00411.2480.3690.3690.0000.0000.0000.000
111A140LEU0-0.006-0.0129.2891.1521.1520.0000.0000.0000.000
112A141ALA0-0.026-0.00912.1870.3210.3210.0000.0000.0000.000
113A142ASP-1-0.915-0.94413.89319.73719.7370.0000.0000.0000.000
114A143MET0-0.022-0.0186.4970.4500.4500.0000.0000.0000.000
115A144ALA0-0.019-0.00311.4040.6610.6610.0000.0000.0000.000
116A145ASP-1-0.891-0.94813.26615.23415.2340.0000.0000.0000.000
117A146VAL0-0.039-0.01612.577-0.647-0.6470.0000.0000.0000.000
118A147MET0-0.020-0.0118.5030.4780.4780.0000.0000.0000.000
119A148ARG10.9320.96213.155-15.712-15.7120.0000.0000.0000.000
120A149LEU0-0.052-0.01216.624-0.994-0.9940.0000.0000.0000.000
121A150LEU0-0.014-0.01013.134-0.848-0.8480.0000.0000.0000.000
122A151SER0-0.029-0.02816.509-0.705-0.7050.0000.0000.0000.000
123A152HIS00.013-0.01217.548-0.304-0.3040.0000.0000.0000.000
124A153LEU0-0.046-0.01617.492-0.673-0.6730.0000.0000.0000.000
125A154LYS10.8890.92415.833-17.524-17.5240.0000.0000.0000.000
126A155ILE00.0630.04419.676-0.628-0.6280.0000.0000.0000.000
127A156VAL0-0.039-0.02622.469-0.688-0.6880.0000.0000.0000.000
128A157GLU-1-0.811-0.87719.99315.11015.1100.0000.0000.0000.000
129A158GLU-1-0.890-0.95419.83613.83013.8300.0000.0000.0000.000
130A159ALA0-0.021-0.00724.323-0.527-0.5270.0000.0000.0000.000
131A160LEU0-0.048-0.03327.003-0.539-0.5390.0000.0000.0000.000
132A161GLU-1-0.826-0.91824.53011.45811.4580.0000.0000.0000.000
133A162ALA0-0.030-0.00927.824-0.383-0.3830.0000.0000.0000.000
134A163VAL0-0.067-0.04630.283-0.398-0.3980.0000.0000.0000.000
135A164LYS10.8210.92428.540-10.725-10.7250.0000.0000.0000.000
136A165ASN0-0.045-0.03028.609-0.443-0.4430.0000.0000.0000.000
137A166ALA00.0180.02632.840-0.142-0.1420.0000.0000.0000.000
138A167THR00.001-0.00835.653-0.119-0.1190.0000.0000.0000.000
139A168ASN0-0.007-0.01338.773-0.312-0.3120.0000.0000.0000.000
140A169GLU-1-0.715-0.84840.6047.3317.3310.0000.0000.0000.000
141A170GLN00.0050.01542.0160.0400.0400.0000.0000.0000.000
142A171ASP-1-0.786-0.88936.8698.3548.3540.0000.0000.0000.000
143A172LEU0-0.0100.01636.4390.2010.2010.0000.0000.0000.000
144A173ALA0-0.020-0.01237.6940.1540.1540.0000.0000.0000.000
145A174ASN0-0.057-0.03435.706-0.103-0.1030.0000.0000.0000.000
146A175ARG10.8220.89032.865-8.752-8.7520.0000.0000.0000.000
147A176PHE00.0340.01433.1890.2650.2650.0000.0000.0000.000
148A177LYS10.8940.93934.789-7.631-7.6310.0000.0000.0000.000
149A178GLU-1-0.863-0.89431.1939.2539.2530.0000.0000.0000.000
150A179PHE00.0770.02629.0990.1910.1910.0000.0000.0000.000
151A180GLY00.0010.00430.4390.2030.2030.0000.0000.0000.000
152A181LYS10.8880.93231.639-8.773-8.7730.0000.0000.0000.000
153A182GLU-1-0.761-0.87326.32811.12711.1270.0000.0000.0000.000
154A183MET00.0060.02127.2600.4400.4400.0000.0000.0000.000
155A184VAL0-0.024-0.00629.1090.0650.0650.0000.0000.0000.000
156A185LYS10.8280.89926.156-10.825-10.8250.0000.0000.0000.000
157A186LEU00.0410.02222.7660.2300.2300.0000.0000.0000.000
158A187ASN0-0.052-0.03925.8130.1700.1700.0000.0000.0000.000
159A188TYR00.0060.01826.4780.0400.0400.0000.0000.0000.000
160A189VAL00.0310.02021.666-0.050-0.0500.0000.0000.0000.000
161A190ALA00.0210.00224.8700.1780.1780.0000.0000.0000.000
162A191ALA0-0.038-0.02425.759-0.046-0.0460.0000.0000.0000.000
163A192ARG10.9040.95224.618-12.222-12.2220.0000.0000.0000.000
164A193ARG10.8520.92019.478-15.386-15.3860.0000.0000.0000.000
165A194GLN00.0380.02524.5630.1960.1960.0000.0000.0000.000
166A195GLN0-0.055-0.03127.361-0.150-0.1500.0000.0000.0000.000
167A196GLU-1-0.853-0.91523.11113.21613.2160.0000.0000.0000.000
168A197LEU0-0.0250.01922.8090.2180.2180.0000.0000.0000.000
169A198LYS10.9560.97725.830-11.894-11.8940.0000.0000.0000.000
170A199ASP-1-0.814-0.90726.47311.36211.3620.0000.0000.0000.000
171A200PRO0-0.013-0.01428.3790.0670.0670.0000.0000.0000.000
172A201HIS00.0110.00027.262-0.446-0.4460.0000.0000.0000.000
173A202CYS00.020-0.00424.7130.2420.2420.0000.0000.0000.000
174A203ARG10.8200.90526.421-10.516-10.5160.0000.0000.0000.000
175A204ASP-1-0.890-0.93829.0239.8159.8150.0000.0000.0000.000
176A205GLU-1-0.885-0.93024.44812.94112.9410.0000.0000.0000.000
177A206MET0-0.028-0.00623.3760.1170.1170.0000.0000.0000.000
178A207ALA0-0.045-0.02326.690-0.121-0.1210.0000.0000.0000.000
179A208ALA00.0000.00229.232-0.218-0.2180.0000.0000.0000.000
180A209ALA00.0110.00925.139-0.177-0.1770.0000.0000.0000.000
181A210ARG10.9030.93027.262-10.819-10.8190.0000.0000.0000.000
182A211GLY0-0.022-0.01428.773-0.277-0.2770.0000.0000.0000.000
183A212ALA0-0.015-0.00928.843-0.308-0.3080.0000.0000.0000.000
184A213LEU00.0330.02225.860-0.241-0.2410.0000.0000.0000.000
185A214LYS10.9440.97729.281-9.049-9.0490.0000.0000.0000.000
186A215LYS10.9480.97432.560-9.088-9.0880.0000.0000.0000.000
187A216ASN00.0600.00630.636-0.467-0.4670.0000.0000.0000.000
188A217ALA00.0630.05231.129-0.085-0.0850.0000.0000.0000.000
189A218THR0-0.076-0.04832.704-0.283-0.2830.0000.0000.0000.000
190A219MET0-0.0140.00434.969-0.226-0.2260.0000.0000.0000.000
191A220LEU00.0480.03230.529-0.198-0.1980.0000.0000.0000.000
192A221TYR00.0030.01834.657-0.156-0.1560.0000.0000.0000.000
193A222THR0-0.011-0.01936.943-0.239-0.2390.0000.0000.0000.000
194A223ALA00.0040.00136.511-0.187-0.1870.0000.0000.0000.000
195A224SER00.000-0.02635.494-0.006-0.0060.0000.0000.0000.000
196A225GLN0-0.052-0.04037.794-0.199-0.1990.0000.0000.0000.000
197A226ALA0-0.041-0.02541.331-0.189-0.1890.0000.0000.0000.000
198A227PHE0-0.025-0.01838.142-0.099-0.0990.0000.0000.0000.000
199A228LEU0-0.027-0.01439.673-0.122-0.1220.0000.0000.0000.000
200A229ARG10.8100.89642.458-7.065-7.0650.0000.0000.0000.000
201A230HIS0-0.0180.00044.525-0.191-0.1910.0000.0000.0000.000
202A231PRO00.0290.02442.4320.1340.1340.0000.0000.0000.000
203A232ASP-1-0.890-0.94542.4726.9816.9810.0000.0000.0000.000
204A233VAL0-0.030-0.00444.3200.0010.0010.0000.0000.0000.000
205A234ALA00.0260.00840.3960.1530.1530.0000.0000.0000.000
206A235ALA00.0170.00139.4360.2350.2350.0000.0000.0000.000
207A236THR0-0.015-0.00839.5810.2400.2400.0000.0000.0000.000
208A237ARG10.9810.99933.061-8.846-8.8460.0000.0000.0000.000
209A238ALA0-0.0120.00235.2560.2860.2860.0000.0000.0000.000
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